How's this? It was difficult to accomplish, and I had to make some compromises, but I managed to move them away from the shadows somewhat. It's hard because they need to be close enough to the atoms so you can tell which name belongs to which atom...
Rearranged the legend a bit, so it should fit better now. Some continent names rearranged as well.
Now that I think of it, this update is actually nothing but a big rearrangement... it shouldn't even have a whole new version number! Oh well, what's done is done...
- Click image to enlarge.

oh, btw, about the idea of bombardment between amide nitrogens, I'll probably discard that idea. Now that I've thought of it, it would seem out of place, just a gimmick that was glued on the map for no other purpose than to have a gimmick on the gameplay.
btw2: with the starting positions & neutrals, the starting territories would go as follows:
(54 territories, out of which 5 blue nitrogens (neutral) and 8 oxygens (starting pos.) = 41 normal territories)
2 players: 13 normal territories each, 15 neutral normal territories, 4 oxygens each, 5 neutral blue nitrogens = 20 neutrals, 17 territories each
3 players: 13 normal territories each, 2 neutral normal territories, 2 oxygens each, 2 neutral oxygens, 5 neutral blue n:s = 9 neutrals, 15 territories each
4 players: 10 normal territories each, 1 neutral normal territory, 2 oxygens each, 5 neutral blue n:s = 6 neutrals, 12 territories each
5 players: 8 normal territories each, 1 neutral normal, 1 oxygen each, 3 neutral oxygens, 5 neutral blue n:s = 9 neutrals, 9 territories each
6 players: 6 normal territories each, 5 neutral normals, 1 oxygen each, 2 neutral oxygens, 5 neutral blues = 12 neutrals, 7 territories each
7 players: 5 normal territories each, 6 neutral normals, 1 oxygen each, 1 neutral oxygen, 5 neutral blues = 12 neutrals, 6 territories each
8 players: 5 normal territories each, 1 neutral normal, 1 oxygen each, 5 neutral blues = 6 neutrals, 6 territories each
How's that?